Creative Collaboration

Reviving the Smell of Extinct Plants

Author: Christina Agapakis

Could we bring back the smell of an extinct flower? Five years ago, this question started us off on an unexpected adventure that’s led us through enormous collections of two hundred year old plant specimens and international art exhibitions, through collaborations with a paleogenomics lab, a smell researcher, and a multidisciplinary artist, and through lots of cutting edge synthetic biology. The culminating immersive installation where you can smell the lost flowers, titled Resurrecting the Sublime, in collaboration with artist Dr. Alexandra Daisy Ginsberg, smell researcher and artist Sissel Tolaas, and with the support of IFF Inc, has been shown at a number of art museums in Europe and will be having its US debut this week as part of Nature—the Cooper Hewitt Design Triennial opening May 10 in New York.

This short film tells the story of Resurrecting the Sublime, from the herbarium to the lab to the art gallery:

A lot of people at Ginkgo and beyond have been involved in bringing this project to life, from the earliest explorations about whether it would be possible with Jason Kakoyiannis all the way through the first exhibition opening. In 2016 I visited the Harvard Herbarium with my former colleague Dawn Thompson on a mission to find extinct plants. Together, we combed the stacks for preserved specimens of plants from the IUCN extinction list. From the more than 5 million samples in the herbarium, we found about a dozen extinct specimens that we could take tiny bits of leaf from. We worked with the UC Santa Cruz Paleogenomics lab to uncover sequences of DNA involved in fragrance production, which our colleague Jue Wang stitched together electronically into two thousand different versions. A team led by organism engineer Christian Ridley used those sequences to build strains of yeast harboring the extinct DNA, and test engineer Scott Marr measured the lost scents each strain made.

We focused our attention on three plants:

The Hibiscadelphus wilderianus Rock, or Maui hau kuahiwi in Hawaiian, was indigenous to ancient lava fields on the southern slopes of Mount Haleakalā, on Maui, Hawaii. Its forest habitat was decimated by colonial cattle ranching, and the final tree was found dying in 1912.

The Orbexilum stipulatum, or Falls-of-the-Ohio Scurfpea, was last seen in 1881 on Rock Island in the Ohio River, near Louisville, Kentucky, before US Dam No. 41 finally flooded its habitat in the 1920s.

The ‘Leucadendron grandiflorum (Salisb.) R. Br.’, the Wynberg Conebush has a more complex story, which we are still uncovering. It was last seen in London in a collector’s garden in 1806; its habitat on Wynberg Hill, in the shadow of Table Mountain, Cape Town, South Africa, was already lost to colonial vineyards. This flower may prove to be completely lost: the project is bringing to light that specimens around the world may historically have been incorrectly identified.

Once we had the list of molecules that the extinct DNA sequences were making in our yeast, we worked with smell researcher Sissel Tolaas to compose those molecules into a complex smell. Sissel used her deep expertise in chemistry and smell to reconstruct the flowers’ smells in her lab, using identical or comparative smell molecules to what we measured in the foundry. Smelling Sissel’s sketches for the first time was magical and uncanny—we were smelling something impossible.

In large scale immersive installations designed by Daisy Ginsberg, fragments of Sissel’s smells diffuse through the air. As you smell the extinct flower and experience the geology of the lost landscape, you become part of an inverted natural history display—the human is the specimen on view.

Resurrecting the Sublime at the St. Etienne Design Biennial. Photo credit: Pierre Grasset.

For me as a biologist, art has been a really important way for me to ask questions and explore the many facets of biotechnology and its place in society. For extinctions that were caused by the actions of humans, asks us to contemplate our actions, and potentially change them for the future. I’m so thrilled to have been able to collaborate with so many brilliant scientists and artists on this project. The experience has been truly sublime. For more info, check out resurrectingthesublime.com.

Posted By: Christina Agapakis

We’re so excited to announce that Yasaman Sheri will be joining us as our secondCreative Resident this fall! Yasaman is a designer exploring the potential for interactions beyond the visual interface, through augmented and virtual reality, sensory, and other biological systems.

Yasaman’s career has spanned many fascinating technologies and systems. She was one of the first designers on the original Microsoft Hololens Operating System team, where she led design interactions on Windows Holographic for five years and designed novel spatial and gestural interfaces for augmented and mixed reality.

Since her time at Microsoft, Yasaman’s research and design work has focused on leveraging her knowledge in machine sensing to expand human experience of sensing and perception. Working with companies like Mozilla, Toyota, and Google X, and teaching at the Copenhagen Institute for Interaction Design and Art Center College of Design, she’s built a unique understanding of sensory design beyond the visual, extending into smell, taste, and haptics.

Student work from Yasaman’s Sensory Design course at the Copenhagen Institute of Interaction Design (header image above is from the same project)

Sensing the environment is fundamental to living things, whether bacteria sensing the gradients of chemical resources in their watery surroundings, snakes sensing the heat of their prey to “see” in the dark, or humans smelling a delicious meal simmering in the kitchen. Biosensors are also fundamental to the study of biochemistry and the practice of synthetic biology: our earliest understandings of gene expression come from studying the system that the bacterium E. coli uses to sense and respond to the presence of lactose sugars, which in turn is used every day in labs to control the function of synthetic gene circuits.

During her time at Ginkgo, Yasaman will explore the design of biosensors in synthetic biology and their potential for intersection with human interaction, bringing her expertise as a designer of sensory experiences and interactive interfaces to this world of biosensors. We’ll be sharing updates from her time at Ginkgo here on the blog and on the Ginkgo Creative Residency Instagram @ginkgocreativeresidency.

Posted By: Christina Agapakis

At the Bioworks2 launch party last month, the Extrapolation Factory set up a pop-up futuristic bio-product assembly line inside the foundry. Guests selected two present-day signals hinting at possible biotech futures and then extrapolated from those signals to imagine a future product. The Extrapolation Factory team did the rest, transforming these ideas into futuristic objects.

Each object, with its bright colors and its 99 cent store packaging, brings together and brings to life complex ideas from the edges of what’s possible today. While very different from the kinds of organisms we’re prototyping in the foundries, the extrapolation exercise is a playful way of pushing the boundaries between imagination and reality.

The products are fun and sometimes silly, but they all tell a story about today’s technologies and their potential. Having this assembly line in our foundry, where we are building some of the present day “signals” was also really interesting. I don’t think we’ll be churning out Poopipes any time soon, but the exercise of imagining the future might help us come up with something equally unexpected.

Check out more photos from the installation on Flickr and learn more about Extrapolation Factory projects on their website.

Posted By: Christina Agapakis

We’re in Ginkgo’s foundry, Bioworks1, attempting to describe the smell of lactones, a family of scents that have a varied character, adding a creamy richness to everything from jasmine flowers to peach gummy candy to luxury perfume. Their smell is difficult to pin down exactly because they are in so many different fragrances and flavors. Lactones are a crucial part of the scent of stone fruits such as plum and peach, blue cheese, butter, coconut scented sunscreen, and the Gucci perfume Rush. They may be milky, buttery, fruity, creamy, fleshy, peachy, and coconutty, often all at once.

These lactones are part of a new palette of cultured ingredients that Ginkgo is producing in collaboration with our partner Robertet, the French fragrance and flavor house based in Grasse and founded in 1850. We’ve already been working with Robertet on creating a “cultured rose”—a rosy mixture of floral, sweet, and spicy scents produced by engineered yeast. With the cultured rose and these lactones there will be a total of ten Ginkgo cultured ingredients on the palette available to Robertet’s perfumers and flavorists.

There are many types of lactones, each with a slightly different structure and a slightly different smell. The peachy penguin smell we sampled first was a ten carbon lactone—decalactone (from deca-, Greek for the number ten, and lactone, from the Latin for milk). Add just one carbon atom to the mix and the smell changes. This undecalactone has the same creamy sweetness as its ten-carbon cousin but it smells lighter, brighter, and fruitier. Add one more carbon to get dodecalactone and the smell changes again: sweet and unctuous, with a deeper caramel and coconut tonality.

Lactones are made biologically when cells break down fatty acids—long chains of carbon and hydrogen plus a few oxygen atoms. As the cell chews up the carbons for energy, the oxygen atoms will spontaneously react and bind part of the long carbon chain back on itself, turning the fatty acid into a closed ring that’s characteristic of lactones. Depending on the length of the fatty acid and the position of the oxygen the cell will make different lactones of the deca- undeca- or dodeca- variety.

Many organisms make lactones as a byproduct of metabolizing fats and oils, from single-celled yeasts to tropical trees. While many of the lactones used in perfumes and flavors used to be extracted from tropical plants—like Massoia trees grown in Papua New Guinea—today the majority are made through chemical processes or yeast fermentation because extracting the lactones from the bark kills the tree.

Making lactones via fermentation is a bit like brewing beer, but instead of the yeast eating sugar and producing alcohol, they eat fatty acids and produce lactones. To make cultured lactones we start with a lactone-producing yeast and tailor their metabolism to focus their production on a single lactone. We do this by changing what the type of fatty acid the yeast eat, and by tuning fatty acid metabolism to make the conversion process more efficient. Designers and fermentation engineers work together to match the right brewing process with the right yeast for each target lactone.

Because the biological process of chewing fatty acids and creating a scent is similar for many different lactones, the lessons we learn from creating one ingredient are generalizable to others, allowing us to efficiently expand the available palette. As we learn more from the biology of flavor and fermentation we’ll be able to design many new scent experiences in collaboration with Robertet and perfumers.